A computational glance of polyurethane biodegradation

Abstract

Our daily lives depend heavily on polyurethane (PU) and other polymers. As PU foam is utilized in so many different areas, polyurethane waste builds up in our surroundings (e.g. water, soil). While there are various methods for managing waste, biodegradation is one that is comparatively underutilized. The benefit of biodegradation is that it may fully mineralize plastic throughout the process and does not require a significant energy input. The drawbacks include the possibility of hazardous chemicals being created during degradation and the possibility that the polymeric product may break down sooner than expected. Microorganisms have been used in several investigations to examine the degradability of polyurethanes. Several living organisms have developed the ability to degrade materials as a result of a protracted time of adaption to polymers as an energy source. Microorganisms require certain enzymes in order to utilise e.g. polyurethane as an energy source. The literature refers to three primary categories of such enzymes: esterase, urease, and lipase, with the last being thought to play a significant role. In this study, all of the bacterial esterase sequences that are currently available are collected, and their homology is assessed by using the BLASTp and AliView tools. Furthermore, those which has a 3D structure were selected and used as host molecules for molecular docking. Model urethanes were prepared by using the GaussView 6.0 software. These structures were optimized at the B3LYP/6-31G(d,p) level of theory by using the Gaussian 09 software package. After the optimization, these molecules were ready to be docked to carefully selected esterases. It is important that not only the ligand molecules have to be optimized, but the proteins must be prepared also, before studying their interactions. As soon as the protein and ligand structures are ready, AutoDock Vina was employed and a standard molecular docking procedure was carried out. The structural and energetical features of the interactions between the enzymes and model urethanes were assessed and the various complexes were compared. By using the results of the sequence analysis and the molecular docking a deeper understanding of polyurethane biodegradation is achieved. However, further analysis is still needed to utilize the full potential of microorganisms in polyurethane waste management.